I think he knew, because A. he’s got a very good intelligence network to begin with, and B. he’s on the ball enough to know that Sansa was smuggled out by Ser Dontos.
As to why not expose the plot, its success actually advances his interests enormously. With Stannis out of the way, Varys’ next task is to destabilize the new regime in advance of his plans with his perfect prince; having one-half of the new regime assassinate the king in a bid to seize control over a child king (who’s not going to produce any inconvenient heirs that might unite the houses by blood), and causing House Lannister to divide against itself through Tyrion’s arrest and trial, helps him enormously.
Thus, Varys can act literally from the shadows: freeing Tyrion and arranging for him to assassinate his father, planting the Gardener coins to stoke Cersei’s paranoia about the Tyrells, assassinating Pycelle and Kevan to prevent them from stabilizing the regime, etc.